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Tuesday, February 24, 2015

I arrived a bit earlier at the year 1 eNanoMapper meeting so that I could sit down with Nina Jealiazkova to work on migrating AMBIT2 to CDK 1.5. One of the big new things is the detection of ring systems, which John gave a major overhaul. Part of that is that the SSSRFinder is now retired into the legacy model. Myself, I haven't even gone into all the new goodies of this, but one of the things we needed to look at, is how to replace the use the SSSRFinder use for finding the SSSR set. So, I just had a check if I understood the replacement code, by using the SSSRFinderTest and replacing the code in those tests with the new code, and all seemed to work as I expect it to do.

So, here are a few examples of code snippets you need to replace. Previously, your code would have something like:

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This blog deals with chemblaics in the broader sense. Chemblaics (pronounced chem-bla-ics) is the science that uses computers to solve problems in chemistry, biochemistry and related fields. The big difference between chemblaics and areas such as chem(o)?informatics, chemometrics, computational chemistry, etc, is that chemblaics only uses open source software, open data, and open standards, making experimental results reproducible and validatable. And this is a big difference!

About Me

Assistant professor at the Dept of Bioinformatics - BiGCaT at NUTRIM, Maastricht University, studying biology at an unsupervised and atomic level. Open Science is my main hobby resulting in participation in, among many others, Bioclipse, CDK and WikiPathways. ORCID:0000-0001-7542-0286. Posts on G+ are personal.

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